One goal of the Section on Drosophila Gene Regulation is to understand the regulation of homeotic gene function in Drosophila. The homeotic genes encode homeodomain-containing transcription factors that control cell fates by regulating the transcription of downstream target genes. The homeotic genes are expressed in precise spatial patterns that are crucial for the proper determination of segmental identities. Cis-acting transcriptional regulatory elements from the homeotic genes have been previously-identified by assays in transgenes in Drosophila. These assays have identified both tissue-specific enhancer elements, as well as cis-regulatory elements that are required for the maintenance of activation or repression throughout development. While these transgene assays have been important in defining the structure of the cis-regulatory elements and identifying trans-acting factors that bind them, their functions within the contexts of the endogenous genes is still not well understood. We have used a large number of existing chromosomal rearrangements in the Sex combs reduced homeotic gene to investigate the functions of the cis-acting elements within the endogenous gene. Characterization of the chromosomal rearrangements revealed that two genomic regions about 70 kb apart in the Sex combs reduced gene must be in cis to maintain proper repression. When not physically linked to each other, these genomic regions interact with regions on the homologous chromosome and cause derepression of its wild-type Sex combs reduced gene. Using a transgene assay, we have identified candidate fragments of DNA that may correspond to these regulatory genomic regions. Both regions appear to contain clusters of regulatory elements that can interact with elements on homologous chromosomes. We deleted two of these candidate elements from the endogenous Sex combs reduced gene by targetted gene replacement. Both deletions only partially disrupt silencing of the Sex combs reduced gene. This suggests that the elements in each cluster have partially redundant functions. Genetic studies identified the Polycomb group of genes that are required for transcriptional silencing. To identify new Polycomb group genes, we have developed a transgene assay using the cis-regulatory elements within the homeotic genes that interact with the Polycomb group proteins. Recessive mutations that disrupt transgene silencing are recovered in mitotic clones in heterozygous flies. We have isolated mutations in most of the known Polycomb group genes on the second chromosome. We have also isolated mutations in several new Polycomb group genes. We have also characterized two regions of the Drosophila genome to identify all genes required for either zygotic viability or male fertility. Only about one-third of the genes in these regions are required for zygotic viability, with another 5% required only for male fertility. Almost two-thirds of the genes do not appear to be essential for either viability or fertility. Within one of these genomic regions, we identified a gene desert (a genomic region that is not required for either viability or fertility.